SNV
Indel
| | Sample minimum | 1 sample | | Arrays supported | Any human Infinium genotyping array including custom and semi-custom to create a SNV VCF output. Illumina provides [Genome FASTA Files](https://help.connected.illumina.com/dragen-array/product-guides/input-files#toc150786139) required to map to the reference genome for human, genome build 37 and 38. DRAGEN Array Cloud offers additional output formats including Locus Summary and Final Report which are applicable for Infinium arrays for human and non-human species. | | Related Local Commands |genotype call
genotype gtc-to-vcf
• IDAT(s)
• Manifest Files \[may be pre-setup on cloud]
• Cluster File \[may be pre-setup on cloud]
• Genome FASTA Files \[pre-setup on cloud]
• Sample Sheet \[optional on cloud and local]
| | Outputs |Per sample:
• SNV VCF File \[optional on cloud and local]
• TBI Index File \[optional on cloud and local]
Per analysis batch:
• Final Report \[cloud only]
• Locus Summary \[cloud only]
| | Cost |Local: No cost download from Illumina Support Site.
Cloud: iCredits to analyze and store data as needed.
| ## DRAGEN Array – PGx – CNV calling | Item | Description | | ----------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Summary | Provides CNV calling on 7 target PGx genes across 10 target regions, plus genotyping outputs. | | Variant types detected |SNV
Indel
CNV
| | Sample minimum | Minimum of 24 samples with 22 passing QC defined as Log R Dev < 0.2. 96 samples are recommended for best results. | | Arrays supported |Check Product & Analysis Compatibility here Product & Analysis Compatibility
See Pharmacogenomic Analysis for semi-custom arrays for further detail.
| | Related Local Commands |genotype call
genotype gtc-to-vcf \[optional]
pgx copy-number call
• IDAT(s)
• Manifest Files \[may be pre-setup on cloud]
• Cluster File \[may be pre-setup on cloud]
• Genome FASTA Files \[pre-setup on cloud]
• PGx CN Model File \[pre-setup on cloud]
• Sample Sheet \[optional on cloud and local]
| | Outputs |Per sample:
• SNV VCF File \[optional on local]
• TBI Index File \[optional on local]
• BedGraph Files \[optional on local]
Per analysis batch:
| | Cost |Local: No cost download from Illumina Support Site.
Cloud: iCredits to analyze and store data as needed.
| ## DRAGEN Array – PGx – Star Allele Annotation | Item | Description | | ----------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | Summary | Provides PGx annotation on over 50 genes, plus PGx CNV and genotyping outputs. | | Variant types detected |SNV
Indel
CNV
Star allele diplotype
| | Sample minimum | Minimum of 24 samples with 22 passing QC defined as Log R Dev < 0.2. 96 samples are recommended for best results. | | Arrays supported |Check Product & Analysis Compatibility here Product & Analysis Compatibility
See Pharmacogenomic Analysis for semi-custom arrays for further detail.
| | Related Local Commands |genotype call
genotype gtc-to-vcf
pgx copy-number call
pgx star-allele call
pgx star-allele annotate
• IDAT(s)
• Manifest Files \[may be pre-setup on cloud]
• Cluster File \[may be pre-setup on cloud]
• Genome FASTA Files \[pre-setup on cloud]
• PGx CN Model File \[pre-setup on cloud]
• PGx Database File \[pre-setup on cloud]
• Sample Sheet \[optional on cloud and local]
| | Outputs |Per sample:
• SNV VCF File \[optional on local]
• TBI Index File \[optional on local]
• BedGraph Files \[optional on local]
Per analysis batch:
| | Cost |Local: Per sample analysis.
Cloud: Per sample analysis. iCredits to store data as needed.
Visit the Illumina Product Page to learn more.
| ## DRAGEN Array – Methylation QC | Item | Description | | ----------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | Summary | Provides methylation QC for Infinium methylation arrays. | | Variant types detected | N/A | | Sample minimum | 1 sample | | Arrays supported | Recommended thresholds and all built-in control probes are available for Methylation Screening Array (MSA) and MethylationEPIC (v1 & v2) originating from iScan. In non-human and custom arrays, availability of built-in QC probes may vary, and failure thresholds must be defined by the user. | | Related Local Commands | Not available on DRAGEN Array Local. | | Related Cloud Specifics | Select Type of Analysis **DRAGEN Array – Methylation – QC** from the dropdown. Adjust customizable thresholds as desired. Further detail can be found in Additional information for [DRAGEN Array Methylation QC](https://help.connected.illumina.com/dragen-array/product-guides/dragen-array-cloud-analysis#dragen-array-methylation-qc). A maximum of 1152 samples are supported. | | Inputs |• IDAT(s) \[from iScan instrument]
• Manifest Files \[may be pre-setup on cloud]
• Sample Sheet \[optional on cloud]
Per sample:
• Methylation Control Probe Output File
• Methylation CG Output File
Per analysis batch:
• Methylation Sample QC Summary Files
• Methylation Sample QC Summary Plots
• Methylation Principal Component Summary
• Methylation Manifest Files
• Methylation Logs and Error Files
CNV
LOH
| | Sample minimum | Minimum of 1 sample. | | Arrays supported | Check Product & Analysis Compatibility here [Product & Analysis Compatibility](#product_compatability) | | Related Local Commands |genotype call
genotype gtc-to-vcf \[optional]
genotype gtc-to-bedgraph
cyto call
cyto annotate
• IDAT(s)
• Manifest Files \[may be pre-setup on cloud]
• Cluster File \[may be pre-setup on cloud]
• Cytogenetics Model File \[pre-setup on cloud]
• Cytogenetics Database File \[only necessary for local]
• Sample Sheet \[optional]
| | Outputs |Per sample:
• Genotype Call (GTC) File \[optional on cloud]
• SNV VCF File \[optional on local and cloud]
• TBI Index File \[optional on local and cloud for snv vcf]
• Cytogenetics Annotation JSON File
• BedGraph Files \[optional on local]
Per analysis batch:
| | Cost |Local: No cost download from Illumina Support Site.
Cloud: iCredits to analyze and store data as needed.
| ## DRAGEN Array - Cytogenetics analysis + Emedgene interpretation | Item | Description | | ----------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Summary | Provides cytogenetic genome-wide copy number and loss of heterozygosity calling. This analysis type integrates with Emedgene via [Automatic Case Creation from ICA](https://help.emg.illumina.com/emedgene-analyze-manual/integrations/automatic-case-creation-from-ica-cyto-array-analysis) on cloud only. | | Variant types detected |CNV
LOH
| | Sample minimum | Minimum of 1 sample. | | Arrays supported | Check Product & Analysis Compatibility here [Product & Analysis Compatibility](#product_compatability) | | Related Local Commands | Not available on DRAGEN Array Local. | | Related Cloud Specifics | Select Type of Analysis **DRAGEN Array - Cytogenetics analysis + Emedgene interpretation** from the dropdown. Max 1152 samples are supported. | | Inputs |• IDAT(s)
• Manifest Files \[may be pre-setup]
• Cluster File \[may be pre-setup]
• Cytogenetics Model File \[may be pre-setup]
• Sample Sheet \[optional]
| | Outputs |Per sample:
• Genotype Call (GTC) File \[optional]
• SNV VCF File \[optional]
• TBI Index File \[optional for snv vcf]
• Cytogenetics Annotation JSON File
Per analysis batch:
| | Cost | Cloud: [iCredits](https://www.illumina.com/products/by-type/informatics-products/icredits.html) to analyze and store data as needed. As well as additional sample-based costs if uploaded into the [Emedgene](https://help.connected.illumina.com/emedgene) interface. |